Align Glutamate/aspartate import permease protein GltK (characterized)
to candidate WP_086510333.1 BZY95_RS12915 glutamine ABC transporter permease GlnP
Query= SwissProt::P0AER5 (224 letters) >NCBI__GCF_002151265.1:WP_086510333.1 Length = 218 Score = 120 bits (301), Expect = 2e-32 Identities = 71/218 (32%), Positives = 120/218 (55%), Gaps = 7/218 (3%) Query: 5 DWSSIVPSLPYLLDGLVITLKITVTAVVIGILWGTMLAVMRLSSFAPVAWFAKAYVNVFR 64 DWS IV +P LL G +T+ ITV + G++ G + +MR + + A Y+ V R Sbjct: 4 DWSVIVTFMPQLLKGAQMTIFITVVGLCGGMVVGAIAGIMRAYGNWLLNYTAMVYIEVIR 63 Query: 65 SIPLVMVLLWFYLIVPGFLQNVLGLSPKNDIRLISAMVAFSMFEAAYYSEIIRAGIQSIS 124 P+V+ +++ Y +P + + P L +AM+A + AY +EI+R +QSIS Sbjct: 64 GTPIVVQVMFLYFALPVLAS--IRIDP-----LSAAMIAIVINAGAYIAEIVRGSLQSIS 116 Query: 125 RGQSSAALALGMTHWQSMKLIILPQAFRAMVPLLLTQGIVLFQDTSLVYVLSLADFFRTA 184 RG + A LALG+ W+ + I+ P AFR ++P L Q I+ +DTSL V+ + + RT Sbjct: 117 RGLAEAGLALGLPRWKVLLYIVGPLAFRRLIPPLGNQFIISLKDTSLFIVIGVGELTRTG 176 Query: 185 STIGERDGTQVEMILFAGFVYFVISLSASLLVSYLKRR 222 I + VE+ +Y +++ S +L++ +++RR Sbjct: 177 QEIMAANFRAVEIWSAIAIMYLIMTGSLTLMLRFIERR 214 Lambda K H 0.330 0.140 0.412 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 128 Number of extensions: 9 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 224 Length of database: 218 Length adjustment: 22 Effective length of query: 202 Effective length of database: 196 Effective search space: 39592 Effective search space used: 39592 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 45 (21.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory